ProteoWizard
|
Namespaces | |
namespace | AminoAcid |
scope for types related to amino acids | |
namespace | examples |
Classes | |
struct | PeptideDatabaseFormula |
struct | PeptideDatabaseRecord |
class | PeptideDatabase |
class | DefaultReaderList |
default Reader list More... | |
struct | DiffConfig |
configuration struct for diffs More... | |
class | DigestedPeptide |
peptide subclass that contains extra metadata provided by digestion More... | |
class | Digestion |
enumerates the peptides from proteolytic digestion of a polypeptide or protein; More... | |
class | Modification |
represents a post-translational modification (PTM) modification formula or masses must be provided at instantiation More... | |
class | ModificationList |
represents a list of modifications on a single amino acid More... | |
class | ModificationMap |
maps peptide/protein sequence indexes (0-based) to a modification list More... | |
class | Peptide |
represents a peptide or polypeptide (a sequence of amino acids) More... | |
class | Fragmentation |
provides fragment ion masses for a peptide More... | |
class | ProteinListCache |
adds a level of flexible MRU caching to a ProteinList processor chain More... | |
class | ProteinListWrapper |
Inheritable pass-through implementation for wrapping a ProteinList. More... | |
struct | Protein |
class | IndexList |
class | ProteinList |
struct | ProteinListSimple |
struct | ProteomeData |
struct | ProteomeDataFile |
ProteomeData object plus file I/O. More... | |
class | Reader |
interface for file readers More... | |
class | ReaderFail |
class | ReaderList |
Reader container (composite pattern). More... | |
class | Reader_FASTA |
FASTA -> ProteomeData stream serialization. More... | |
class | Serializer_FASTA |
ProteomeData <-> FASTA stream serialization. More... | |
class | TextWriter |
struct | Version |
class | IPIFASTADatabase |
class for accessing data in ipi.*.fasta files More... |
Typedefs | |
typedef boost::shared_ptr < Protein > | ProteinPtr |
typedef boost::shared_ptr < ProteinList > | ProteinListPtr |
typedef boost::shared_ptr< Reader > | ReaderPtr |
Functions | |
PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const PeptideDatabaseFormula &formula) |
PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const PeptideDatabaseRecord &record) |
PWIZ_API_DECL bool | operator== (const PeptideDatabaseFormula &r, const PeptideDatabaseFormula &s) |
PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const data::Diff< ProteomeData, DiffConfig > &diff) |
PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, ProteomeDataFile::Format format) |
PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const ProteomeDataFile::WriteConfig &config) |
PWIZ_API_DECL ReaderList | operator+ (const ReaderPtr &lhs, const ReaderPtr &rhs) |
returns a list containing the lhs and rhs as readers | |
PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const Reader_FASTA::Config &config) |
PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const IPIFASTADatabase::Record &record) |
typedef boost::shared_ptr<Protein> pwiz::proteome::ProteinPtr |
Definition at line 48 of file ProteomeData.hpp.
typedef boost::shared_ptr<ProteinList> pwiz::proteome::ProteinListPtr |
Definition at line 73 of file ProteomeData.hpp.
typedef boost::shared_ptr<Reader> pwiz::proteome::ReaderPtr |
Definition at line 89 of file Reader.hpp.
PWIZ_API_DECL std::ostream& pwiz::proteome::operator<< | ( | std::ostream & | os, |
const PeptideDatabaseFormula & | formula | ||
) |
PWIZ_API_DECL std::ostream& pwiz::proteome::operator<< | ( | std::ostream & | os, |
const PeptideDatabaseRecord & | record | ||
) |
PWIZ_API_DECL bool pwiz::proteome::operator== | ( | const PeptideDatabaseFormula & | r, |
const PeptideDatabaseFormula & | s | ||
) |
PWIZ_API_DECL std::ostream& pwiz::proteome::operator<< | ( | std::ostream & | os, |
const data::Diff< ProteomeData, DiffConfig > & | diff | ||
) |
PWIZ_API_DECL std::ostream& pwiz::proteome::operator<< | ( | std::ostream & | os, |
ProteomeDataFile::Format | format | ||
) |
PWIZ_API_DECL std::ostream& pwiz::proteome::operator<< | ( | std::ostream & | os, |
const ProteomeDataFile::WriteConfig & | config | ||
) |
PWIZ_API_DECL ReaderList pwiz::proteome::operator+ | ( | const ReaderPtr & | lhs, |
const ReaderPtr & | rhs | ||
) |
returns a list containing the lhs and rhs as readers
PWIZ_API_DECL std::ostream& pwiz::proteome::operator<< | ( | std::ostream & | os, |
const Reader_FASTA::Config & | config | ||
) |
PWIZ_API_DECL std::ostream& pwiz::proteome::operator<< | ( | std::ostream & | os, |
const IPIFASTADatabase::Record & | record | ||
) |